[{"type":"conference","fulldoi":"https://doi.org/10.1109/SiPS.2018.8598402","language":[{"iso":"eng"}],"isi":1,"month":"12","scopus_import":"1","doi":"10.1109/SiPS.2018.8598402","date_published":"2018-12-31T00:00:00Z","author":[{"first_name":"Alen","last_name":"Stojanov","full_name":"Stojanov, Alen"},{"first_name":"Tyler Michael","full_name":"Smith, Tyler Michael","last_name":"Smith"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"Markus","full_name":"Puschel, Markus","last_name":"Puschel"}],"department":[{"_id":"DaAl"}],"article_processing_charge":"No","article_number":"8598402","external_id":{"isi":["000465106800060"]},"_id":"6031","day":"31","citation":{"chicago":"Stojanov, Alen, Tyler Michael Smith, Dan-Adrian Alistarh, and Markus Puschel. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” In 2018 IEEE International Workshop on Signal Processing Systems, Vol. 2018–October. IEEE, 2018. https://doi.org/10.1109/SiPS.2018.8598402.","mla":"Stojanov, Alen, et al. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” 2018 IEEE International Workshop on Signal Processing Systems, vol. 2018–October, 8598402, IEEE, 2018, doi:10.1109/SiPS.2018.8598402.","ista":"Stojanov A, Smith TM, Alistarh D-A, Puschel M. 2018. Fast quantized arithmetic on x86: Trading compute for data movement. 2018 IEEE International Workshop on Signal Processing Systems. SiPS: Workshop on Signal Processing Systems vol. 2018–October, 8598402.","short":"A. Stojanov, T.M. Smith, D.-A. Alistarh, M. Puschel, in:, 2018 IEEE International Workshop on Signal Processing Systems, IEEE, 2018.","ama":"Stojanov A, Smith TM, Alistarh D-A, Puschel M. Fast quantized arithmetic on x86: Trading compute for data movement. In: 2018 IEEE International Workshop on Signal Processing Systems. Vol 2018-October. IEEE; 2018. doi:10.1109/SiPS.2018.8598402","ieee":"A. Stojanov, T. M. Smith, D.-A. Alistarh, and M. Puschel, “Fast quantized arithmetic on x86: Trading compute for data movement,” in 2018 IEEE International Workshop on Signal Processing Systems, Cape Town, South Africa, 2018, vol. 2018–October.","apa":"Stojanov, A., Smith, T. M., Alistarh, D.-A., & Puschel, M. (2018). Fast quantized arithmetic on x86: Trading compute for data movement. In 2018 IEEE International Workshop on Signal Processing Systems (Vol. 2018–October). Cape Town, South Africa: IEEE. https://doi.org/10.1109/SiPS.2018.8598402"},"quality_controlled":"1","volume":"2018-October","publication":"2018 IEEE International Workshop on Signal Processing Systems","publication_status":"published","oa_version":"None","publisher":"IEEE","abstract":[{"lang":"eng","text":"We introduce Clover, a new library for efficient computation using low-precision data, providing mathematical routines required by fundamental methods in optimization and sparse recovery. Our library faithfully implements variants of stochastic quantization that guarantee convergence at low precision, and supports data formats from 4-bit quantized to 32-bit IEEE-754 on current Intel processors. In particular, we show that 4-bit can be implemented efficiently using Intel AVX despite the lack of native support for this data format. Experimental results with dot product, matrix-vector multiplication (MVM), gradient descent (GD), and iterative hard thresholding (IHT) demonstrate that the attainable speedups are in many cases close to linear with respect to the reduction of precision due to reduced data movement. Finally, for GD and IHT, we show examples of absolute speedup achieved by 4-bit versus 32-bit, by iterating until a given target error is achieved."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","status":"public","title":"Fast quantized arithmetic on x86: Trading compute for data movement","date_created":"2019-02-17T22:59:25Z","conference":{"start_date":"2018-10-21","location":"Cape Town, South Africa","name":"SiPS: Workshop on Signal Processing Systems","end_date":"2018-10-24"},"date_updated":"2023-09-19T14:41:51Z"},{"abstract":[{"lang":"eng","text":"The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids."}],"year":"2018","status":"public","title":"Even delta-matroids and the complexity of planar boolean CSPs","_id":"6032","publication":"ACM Transactions on Algorithms","quality_controlled":"1","citation":{"mla":"Kazda, Alexandr, et al. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms, vol. 15, no. 2, 22, ACM, 2018, doi:10.1145/3230649.","chicago":"Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms. ACM, 2018. https://doi.org/10.1145/3230649.","short":"A. Kazda, V. Kolmogorov, M. Rolinek, ACM Transactions on Algorithms 15 (2018).","ista":"Kazda A, Kolmogorov V, Rolinek M. 2018. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 15(2), 22.","ama":"Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 2018;15(2). doi:10.1145/3230649","ieee":"A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar boolean CSPs,” ACM Transactions on Algorithms, vol. 15, no. 2. ACM, 2018.","apa":"Kazda, A., Kolmogorov, V., & Rolinek, M. (2018). Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3230649"},"day":"01","publication_status":"published","doi":"10.1145/3230649","date_published":"2018-12-01T00:00:00Z","arxiv":1,"external_id":{"isi":["000468036500007"],"arxiv":["1602.03124"]},"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.03124"}],"ec_funded":1,"month":"12","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2019-02-17T22:59:25Z","related_material":{"record":[{"status":"public","id":"1192","relation":"earlier_version"}]},"date_updated":"2025-06-04T08:46:58Z","volume":15,"article_type":"original","oa_version":"Preprint","publisher":"ACM","oa":1,"scopus_import":"1","department":[{"_id":"VlKo"}],"author":[{"last_name":"Kazda","full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr"},{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal"}],"article_processing_charge":"No","article_number":"22","intvolume":" 15","issue":"2","fulldoi":"https://doi.org/10.1145/3230649","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160"}],"language":[{"iso":"eng"}]},{"volume":35,"oa_version":"Submitted Version","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:47:27Z","date_updated":"2023-09-19T10:39:09Z","issue":"5","intvolume":" 35","fulldoi":"https://doi.org/10.1016/j.anihpc.2017.11.004","language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","department":[{"_id":"JuFi"}],"article_processing_charge":"No","author":[{"first_name":"Mitia","last_name":"Duerinckx","full_name":"Duerinckx, Mitia"},{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L"}],"_id":"606","quality_controlled":"1","publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","citation":{"ieee":"M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.","ama":"Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004","apa":"Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004","chicago":"Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.","mla":"Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004.","ista":"Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319.","short":"M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319."},"day":"01","publication_status":"published","abstract":[{"lang":"eng","text":"We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data."}],"year":"2018","title":"Well-posedness for mean-field evolutions arising in superconductivity","status":"public","acknowledgement":"The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00268"}],"page":"1267-1319","month":"08","publist_id":"7199","isi":1,"doi":"10.1016/j.anihpc.2017.11.004","date_published":"2018-08-01T00:00:00Z","arxiv":1,"external_id":{"arxiv":["1607.00268"],"isi":["000437975500005"]}},{"fulldoi":"https://doi.org/10.1016/j.physd.2017.10.015","language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"author":[{"first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","last_name":"Bodova"},{"last_name":"Haskovec","full_name":"Haskovec, Jan","first_name":"Jan"},{"last_name":"Markowich","full_name":"Markowich, Peter","first_name":"Peter"}],"article_processing_charge":"No","volume":"376-377","oa_version":"Submitted Version","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:47:28Z","date_updated":"2024-10-09T20:58:45Z","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.08757"}],"page":"108-120","publist_id":"7198","month":"08","isi":1,"date_published":"2018-08-01T00:00:00Z","doi":"10.1016/j.physd.2017.10.015","arxiv":1,"external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"_id":"607","quality_controlled":"1","publication":"Physica D: Nonlinear Phenomena","day":"01","citation":{"apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015."},"publication_status":"published","year":"2018","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"corr_author":"1","status":"public","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n"},{"volume":712,"ddc":["000"],"publisher":"Elsevier","article_type":"original","oa_version":"Published Version","date_created":"2018-12-11T11:47:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-18T18:58:53Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"fulldoi":"https://doi.org/10.1016/j.tcs.2017.11.001","intvolume":" 712","language":[{"iso":"eng"}],"author":[{"full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"department":[{"_id":"ToHe"}],"article_processing_charge":"No","scopus_import":"1","oa":1,"publication":"Theoretical Computer Science","quality_controlled":"1","day":"15","citation":{"apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001."},"_id":"608","publication_status":"published","corr_author":"1","status":"public","title":"Synthesis from component libraries with costs","abstract":[{"lang":"eng","text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game."}],"year":"2018","page":"50 - 72","ec_funded":1,"type":"journal_article","main_file_link":[{"open_access":"1","url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529"}],"month":"02","publist_id":"7197","isi":1,"date_published":"2018-02-15T00:00:00Z","doi":"10.1016/j.tcs.2017.11.001","external_id":{"isi":["000424959200003"]}},{"date_updated":"2021-01-12T08:06:06Z","extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:25Z","oa_version":"Preprint","publisher":"Springer","oa":1,"author":[{"first_name":"Andriy","last_name":"Bondarenko","full_name":"Bondarenko, Andriy"},{"last_name":"Mellit","full_name":"Mellit, Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"},{"last_name":"Prymak","full_name":"Prymak, Andriy","first_name":"Andriy"},{"first_name":"Danylo","last_name":"Radchenko","full_name":"Radchenko, Danylo"},{"first_name":"Maryna","full_name":"Viazovska, Maryna","last_name":"Viazovska"}],"article_processing_charge":"No","department":[{"_id":"TaHa"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1007/978-3-319-72456-0_7","year":"2018","abstract":[{"text":"We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. ","lang":"eng"}],"title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","status":"public","publication_status":"published","_id":"61","day":"23","citation":{"apa":"Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7","ieee":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","ama":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7","ista":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134.","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","chicago":"Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7.","mla":"Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7."},"quality_controlled":"1","publication":"Contemporary Computational Mathematics","external_id":{"arxiv":["1509.06286"]},"date_published":"2018-05-23T00:00:00Z","doi":"10.1007/978-3-319-72456-0_7","arxiv":1,"publist_id":"7993","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1509.06286","open_access":"1"}],"type":"book_chapter","page":"131 - 134"},{"has_accepted_license":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"checksum":"540f941e8d3530a9441e4affd94f07d7","relation":"main_file","file_name":"IST-2018-978-v1+1_elife-32073-v1.pdf","file_id":"4832","date_updated":"2020-07-14T12:47:20Z","file_size":1435585,"creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:10:43Z","access_level":"open_access"}],"_id":"616","day":"09","citation":{"chicago":"Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse, Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073.","mla":"Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife Sciences Publications, 2018, doi:10.7554/eLife.32073.","short":"C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt, M. Brown, S. Cremer, ELife 7 (2018).","ista":"Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 7, e32073.","ieee":"C. Pull et al., “Destructive disinfection of infected brood prevents systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences Publications, 2018.","ama":"Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 2018;7. doi:10.7554/eLife.32073","apa":"Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt, T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073"},"publication":"eLife","quality_controlled":"1","abstract":[{"lang":"eng","text":"Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − "destructive disinfection" − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation."}],"year":"2018","title":"Destructive disinfection of infected brood prevents systemic disease spread in ant colonies","status":"public","corr_author":"1","isi":1,"month":"01","publist_id":"7188","type":"journal_article","ec_funded":1,"external_id":{"isi":["000419601300001"]},"date_published":"2018-01-09T00:00:00Z","doi":"10.7554/eLife.32073","oa_version":"Published Version","publisher":"eLife Sciences Publications","ddc":["570","590"],"file_date_updated":"2020-07-14T12:47:20Z","volume":7,"related_material":{"record":[{"relation":"dissertation_contains","id":"819","status":"public"}]},"date_updated":"2026-04-08T14:19:10Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:47:31Z","language":[{"iso":"eng"}],"intvolume":" 7","fulldoi":"https://doi.org/10.7554/eLife.32073","project":[{"grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","grant_number":"302004"}],"pubrep_id":"978","article_number":"e32073","oa":1,"scopus_import":"1","article_processing_charge":"Yes","author":[{"last_name":"Pull","full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher"},{"last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","first_name":"Line V"},{"full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer","first_name":"Florian","id":"39523C54-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"last_name":"Tragust","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Thomas","full_name":"Schmitt, Thomas","last_name":"Schmitt"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"SyCr"}]},{"publication":"Journal of Evolutionary Biology","quality_controlled":"1","citation":{"chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211.","mla":"Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31, no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.","short":"M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018) 159–171.","ista":"Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 31(1), 159–171.","ama":"Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 2018;31(1):159-171. doi:10.1111/jeb.13211","ieee":"M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211"},"day":"01","_id":"617","publication_status":"published","title":"Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance","status":"public","year":"2018","abstract":[{"text":"Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions.","lang":"eng"}],"acknowledgement":"We would like to thank Susann Wicke for performing the genome-wide SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG) priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR 872/1-1). ","page":"159 - 171","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13211"}],"publist_id":"7187","month":"01","isi":1,"date_published":"2018-01-01T00:00:00Z","doi":"10.1111/jeb.13211","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"external_id":{"pmid":["29150962"],"isi":["000419307000014"]},"volume":31,"ddc":["570"],"publisher":"Wiley","pmid":1,"article_type":"original","oa_version":"Published Version","date_created":"2018-12-11T11:47:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-18T19:00:18Z","fulldoi":"https://doi.org/10.1111/jeb.13211","intvolume":" 31","issue":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"SyCr"}],"author":[{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","first_name":"Megan","orcid":"0000-0002-8696-6978","last_name":"Kutzer","full_name":"Kutzer, Megan"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"first_name":"Sophie","last_name":"Armitage","full_name":"Armitage, Sophie"}],"scopus_import":"1","oa":1},{"acknowledgement":"Partially funded by ERC Advanced Grant RANMAT No. 338804.\r\nPartially supported by the Hausdorff Center for Mathematics.\r\n","status":"public","title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","abstract":[{"text":"We study the unique solution $m$ of the Dyson equation \\[ -m(z)^{-1} = z - a\r\n+ S[m(z)] \\] on a von Neumann algebra $\\mathcal{A}$ with the constraint\r\n$\\mathrm{Im}\\,m\\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is\r\na self-adjoint element of $\\mathcal{A}$ and $S$ is a positivity-preserving\r\nlinear operator on $\\mathcal{A}$. We show that $m$ is the Stieltjes transform\r\nof a compactly supported $\\mathcal{A}$-valued measure on $\\mathbb{R}$. Under\r\nsuitable assumptions, we establish that this measure has a uniformly\r\n$1/3$-H\\\"{o}lder continuous density with respect to the Lebesgue measure, which\r\nis supported on finitely many intervals, called bands. In fact, the density is\r\nanalytic inside the bands with a square-root growth at the edges and internal\r\ncubic root cusps whenever the gap between two bands vanishes. The shape of\r\nthese singularities is universal and no other singularity may occur. We give a\r\nprecise asymptotic description of $m$ near the singular points. These\r\nasymptotics generalize the analysis at the regular edges given in the companion\r\npaper on the Tracy-Widom universality for the edge eigenvalue statistics for\r\ncorrelated random matrices [arXiv:1804.07744] and they play a key role in the\r\nproof of the Pearcey universality at the cusp for Wigner-type matrices\r\n[arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band\r\nmass formula from [arXiv:1804.07744] to the von Neumann algebra setting by\r\nshowing that the spectral mass of the bands is topologically rigid under\r\ndeformations and we conclude that these masses are quantized in some important\r\ncases.","lang":"eng"}],"year":"2018","publication_status":"draft","citation":{"apa":"Alt, J., Erdös, L., & Krüger, T. H. (n.d.). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv. https://doi.org/10.48550/arXiv.1804.07752","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv. doi:10.48550/arXiv.1804.07752","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” arXiv. .","ista":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. arXiv, 1804.07752.","short":"J. Alt, L. Erdös, T.H. Krüger, ArXiv (n.d.).","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, 1804.07752, doi:10.48550/arXiv.1804.07752.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1804.07752."},"day":"20","publication":"arXiv","_id":"6183","external_id":{"arxiv":["1804.07752"]},"arxiv":1,"date_published":"2018-04-20T00:00:00Z","doi":"10.48550/arXiv.1804.07752","month":"04","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07752"}],"type":"preprint","date_updated":"2026-04-08T14:11:36Z","related_material":{"record":[{"id":"14694","relation":"later_version","status":"public"},{"relation":"dissertation_contains","id":"149","status":"public"}]},"date_created":"2019-03-28T09:20:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_number":"1804.07752","department":[{"_id":"LaEr"}],"article_processing_charge":"No","author":[{"full_name":"Alt, Johannes","last_name":"Alt","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"orcid":"0000-0002-4821-3297","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H","last_name":"Krüger"}],"oa":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.48550/arXiv.1804.07752","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"}]},{"language":[{"iso":"eng"}],"month":"09","isi":1,"type":"conference","fulldoi":"https://doi.org/10.1109/icra.2018.8461106","external_id":{"isi":["000446394503031"]},"article_number":"8461106","publication_identifier":{"isbn":["9781538630815"]},"doi":"10.1109/icra.2018.8461106","scopus_import":"1","date_published":"2018-09-10T00:00:00Z","article_processing_charge":"No","author":[{"first_name":"Maria","last_name":"Pozzi","full_name":"Pozzi, Maria"},{"full_name":"Miguel Villalba, Eder","last_name":"Miguel Villalba","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5665-0430"},{"full_name":"Deimel, Raphael","last_name":"Deimel","first_name":"Raphael"},{"first_name":"Monica","last_name":"Malvezzi","full_name":"Malvezzi, Monica"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"last_name":"Brock","full_name":"Brock, Oliver","first_name":"Oliver"},{"first_name":"Domenico","full_name":"Prattichizzo, Domenico","last_name":"Prattichizzo"}],"department":[{"_id":"BeBi"}],"publication_status":"published","oa_version":"None","publisher":"IEEE","_id":"6195","quality_controlled":"1","day":"10","citation":{"apa":"Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock, O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots modeled as kinematic chains. Presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106","ama":"Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106","ieee":"M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled as kinematic chains,” presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia, 2018.","ista":"Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains. ICRA: International Conference on Robotics and Automation, 8461106.","short":"M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock, D. Prattichizzo, in:, IEEE, 2018.","chicago":"Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106.","mla":"Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106."},"date_updated":"2023-09-19T14:49:03Z","conference":{"end_date":"2018-05-25","name":"ICRA: International Conference on Robotics and Automation","location":"Brisbane, Australia","start_date":"2018-05-21"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"In the context of robotic manipulation and grasping, the shift from a view that is static (force closure of a single posture) and contact-deprived (only contact for force closure is allowed, everything else is obstacle) towards a view that is dynamic and contact-rich (soft manipulation) has led to an increased interest in soft hands. These hands can easily exploit environmental constraints and object surfaces without risk, and safely interact with humans, but present also some challenges. Designing them is difficult, as well as predicting, modelling, and “programming” their interactions with the objects and the environment. This paper tackles the problem of simulating them in a fast and effective way, leveraging on novel and existing simulation technologies. We present a triple-layered simulation framework where dynamic properties such as stiffness are determined from slow but accurate FEM simulation data once, and then condensed into a lumped parameter model that can be used to fast simulate soft fingers and soft hands. We apply our approach to the simulation of soft pneumatic fingers.","lang":"eng"}],"year":"2018","date_created":"2019-04-04T09:50:38Z","status":"public","title":"Efficient FEM-based simulation of soft robots modeled as kinematic chains"},{"status":"public","title":"Flexible learning-free segmentation and reconstruction of neural volumes","abstract":[{"lang":"eng","text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively."}],"year":"2018","acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.","citation":{"ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.","short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:10.1038/s41598-018-32628-3.","chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-32628-3.","apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3"},"day":"24","quality_controlled":"1","publication":"Scientific Reports","_id":"62","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2018_ScientificReports_Shahbazi.pdf","file_id":"5699","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2","relation":"main_file","content_type":"application/pdf","creator":"dernst","date_created":"2018-12-17T12:22:24Z","access_level":"open_access","date_updated":"2020-07-14T12:47:24Z","file_size":4141645}],"has_accepted_license":"1","publication_status":"published","doi":"10.1038/s41598-018-32628-3","date_published":"2018-09-24T00:00:00Z","external_id":{"isi":["000445336600015"]},"type":"journal_article","isi":1,"publist_id":"7992","month":"09","date_created":"2018-12-11T11:44:25Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-11T14:02:55Z","related_material":{"link":[{"relation":"erratum","url":"http://doi.org/10.1038/s41598-018-36220-7"}]},"volume":8,"file_date_updated":"2020-07-14T12:47:24Z","ddc":["570"],"publisher":"Nature Publishing Group","oa_version":"Published Version","article_type":"original","author":[{"first_name":"Ali","last_name":"Shabazi","full_name":"Shabazi, Ali"},{"first_name":"Jeffery","last_name":"Kinnison","full_name":"Kinnison, Jeffery"},{"first_name":"Rafael","full_name":"Vescovi, Rafael","last_name":"Vescovi"},{"last_name":"Du","full_name":"Du, Ming","first_name":"Ming"},{"first_name":"Robert","last_name":"Hill","full_name":"Hill, Robert"},{"last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"},{"last_name":"Takeno","full_name":"Takeno, Marc","first_name":"Marc"},{"last_name":"Zeng","full_name":"Zeng, Hongkui","first_name":"Hongkui"},{"first_name":"Nuno","full_name":"Da Costa, Nuno","last_name":"Da Costa"},{"first_name":"Jaime","full_name":"Grutzendler, Jaime","last_name":"Grutzendler"},{"full_name":"Kasthuri, Narayanan","last_name":"Kasthuri","first_name":"Narayanan"},{"full_name":"Scheirer, Walter","last_name":"Scheirer","first_name":"Walter"}],"department":[{"_id":"MaJö"}],"article_processing_charge":"No","oa":1,"scopus_import":"1","article_number":"14247","fulldoi":"https://doi.org/10.1038/s41598-018-32628-3","issue":"1","intvolume":" 8","language":[{"iso":"eng"}]},{"status":"public","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","abstract":[{"text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.","lang":"eng"}],"year":"2018","citation":{"ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.","mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696"},"day":"04","publication":"Journal of Cell Science","quality_controlled":"1","_id":"620","publication_status":"published","doi":"10.1242/jcs.207696","date_published":"2018-01-04T00:00:00Z","external_id":{"pmid":["29192062"],"isi":["000424786900012"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062","open_access":"1"}],"type":"journal_article","isi":1,"publist_id":"7184","month":"01","date_created":"2018-12-11T11:47:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-18T19:01:31Z","volume":131,"ddc":["570"],"pmid":1,"publisher":"Company of Biologists","oa_version":"Published Version","department":[{"_id":"DaSi"}],"article_processing_charge":"No","author":[{"first_name":"Wataru","last_name":"Yamamoto","full_name":"Yamamoto, Wataru"},{"last_name":"Wada","full_name":"Wada, Suguru","first_name":"Suguru"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"last_name":"Aoshima","full_name":"Aoshima, Kaito","first_name":"Kaito"},{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Junko","full_name":"Toshima, Junko","last_name":"Toshima"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"oa":1,"scopus_import":"1","article_number":"jcs207696","fulldoi":"https://doi.org/10.1242/jcs.207696","issue":"1","intvolume":" 131","language":[{"iso":"eng"}]},{"external_id":{"isi":["000448656700018"]},"doi":"10.3390/genes9100480","date_published":"2018-10-04T00:00:00Z","isi":1,"month":"10","publist_id":"7991","type":"journal_article","ec_funded":1,"acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","year":"2018","abstract":[{"text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.","lang":"eng"}],"title":"Unusual diversity of sex chromosomes in African cichlid fishes","status":"public","has_accepted_license":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"5743","file_name":"2018_Genes_Gammerdinger.pdf","checksum":"bec527692e2c9b56919c0429634ff337","relation":"main_file","date_created":"2018-12-18T09:54:46Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:47:27Z","file_size":1415791}],"_id":"63","citation":{"ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI, 2018.","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI. https://doi.org/10.3390/genes9100480","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI, 2018. https://doi.org/10.3390/genes9100480.","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI, 2018, doi:10.3390/genes9100480.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480."},"day":"04","publication":"Genes","quality_controlled":"1","article_number":"480","oa":1,"scopus_import":"1","author":[{"first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","full_name":"Gammerdinger, William J","last_name":"Gammerdinger"},{"first_name":"Thomas","full_name":"Kocher, Thomas","last_name":"Kocher"}],"article_processing_charge":"No","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"intvolume":" 9","issue":"10","fulldoi":"https://doi.org/10.3390/genes9100480","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"date_updated":"2025-04-15T06:50:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:26Z","oa_version":"Published Version","publisher":"MDPI","ddc":["570"],"file_date_updated":"2020-07-14T12:47:27Z","volume":9},{"date_created":"2019-04-17T10:53:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T07:59:29Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","relation":"press_release","description":"News on IST Homepage"}]},"volume":121,"publisher":"American Physical Society","oa_version":"Preprint","department":[{"_id":"MiLe"}],"article_processing_charge":"No","author":[{"last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"first_name":"Timur","last_name":"Tscherbul","full_name":"Tscherbul, Timur"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"oa":1,"scopus_import":"1","article_number":"165301","fulldoi":"https://doi.org/10.1103/physrevlett.121.165301","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"issue":"16","intvolume":" 121","language":[{"iso":"eng"}],"status":"public","title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","abstract":[{"lang":"eng","text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment."}],"year":"2018","citation":{"ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301."},"day":"16","publication":"Physical Review Letters","quality_controlled":"1","_id":"6339","publication_status":"published","arxiv":1,"date_published":"2018-10-16T00:00:00Z","doi":"10.1103/physrevlett.121.165301","external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"type":"journal_article","isi":1,"month":"10"},{"quality_controlled":"1","publication":"Bio-Protocol","citation":{"apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018."},"day":"20","_id":"6354","file":[{"file_name":"2018_BioProtocol_Fan.pdf","file_id":"6360","checksum":"d4588377e789da7f360b553ae02c5119","relation":"main_file","content_type":"application/pdf","creator":"dernst","date_created":"2019-04-30T08:04:33Z","access_level":"open_access","date_updated":"2020-07-14T12:47:28Z","file_size":2928337}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","publication_status":"published","corr_author":"1","status":"public","title":"Platelet migration and bacterial trapping assay under flow","abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"year":"2018","DOAJ_listed":"1","acknowledgement":"This protocol was adapted from a previously published study (Gaertner et al., 2017). We thank Michael Lorenz for his excellent assistance in bacteria culture. This work was funded by the DFG SFB 914 (S.M. [B02 and Z01]), the DFG SFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Centre for Cardiovascular Research (DZHK) (MHA 1.4VD [S.M.]), FP7 program (project 260309, PRESTIGE [S.M.]), FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.), Marie Sklodowska Curie Individual Fellowship (EU project 747687, LamelliaActin [F.G.]).","OA_place":"publisher","ec_funded":1,"type":"journal_article","month":"09","doi":"10.21769/bioprotoc.3018","date_published":"2018-09-20T00:00:00Z","publication_identifier":{"issn":["2331-8325"]},"external_id":{"pmid":["34395806"]},"keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"volume":8,"ddc":["570"],"file_date_updated":"2020-07-14T12:47:28Z","pmid":1,"publisher":"Bio-Protocol","article_type":"original","oa_version":"Published Version","date_created":"2019-04-29T09:40:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-20T07:43:06Z","fulldoi":"https://doi.org/10.21769/bioprotoc.3018","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687"}],"intvolume":" 8","issue":"18","language":[{"iso":"eng"}],"article_processing_charge":"Yes","author":[{"first_name":"Shuxia","last_name":"Fan","full_name":"Fan, Shuxia"},{"full_name":"Lorenz, Michael","last_name":"Lorenz","first_name":"Michael"},{"first_name":"Steffen","full_name":"Massberg, Steffen","last_name":"Massberg"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R","orcid":"0000-0001-6120-3723","last_name":"Gärtner","full_name":"Gärtner, Florian R"}],"department":[{"_id":"MiSi"}],"OA_type":"gold","oa":1,"article_number":"e3018"},{"arxiv":1,"date_published":"2018-05-31T00:00:00Z","doi":"10.1017/fms.2018.7","publication_identifier":{"issn":["2050-5094"]},"external_id":{"isi":["000433915500001"],"arxiv":["1712.10205"]},"ec_funded":1,"type":"journal_article","isi":1,"month":"05","title":"Any cyclic quadrilateral can be inscribed in any closed convex smooth curve","status":"public","corr_author":"1","year":"2018","abstract":[{"lang":"eng","text":"We prove that any cyclic quadrilateral can be inscribed in any closed convex C1-curve. The smoothness condition is not required if the quadrilateral is a rectangle."}],"day":"31","citation":{"ama":"Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 2018;6. doi:10.1017/fms.2018.7","ieee":"A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in any closed convex smooth curve,” Forum of Mathematics, Sigma, vol. 6. Cambridge University Press, 2018.","apa":"Akopyan, A., & Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2018.7","chicago":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma. Cambridge University Press, 2018. https://doi.org/10.1017/fms.2018.7.","mla":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma, vol. 6, e7, Cambridge University Press, 2018, doi:10.1017/fms.2018.7.","ista":"Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7.","short":"A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018)."},"publication":"Forum of Mathematics, Sigma","quality_controlled":"1","_id":"6355","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2019-04-30T06:14:58Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:47:28Z","file_size":249246,"file_id":"6356","file_name":"2018_ForumMahtematics_Akopyan.pdf","checksum":"5a71b24ba712a3eb2e46165a38fbc30a","relation":"main_file"}],"has_accepted_license":"1","publication_status":"published","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"JaMa"}],"author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","orcid":"0000-0002-7840-5062","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"}],"article_processing_charge":"No","oa":1,"article_number":"e7","fulldoi":"https://doi.org/10.1017/fms.2018.7","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"intvolume":" 6","language":[{"iso":"eng"}],"date_created":"2019-04-30T06:09:57Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2026-04-08T07:25:54Z","related_material":{"record":[{"id":"8156","relation":"dissertation_contains","status":"public"}]},"volume":6,"file_date_updated":"2020-07-14T12:47:28Z","ddc":["510"],"publisher":"Cambridge University Press","oa_version":"Published Version"},{"issue":"35","intvolume":" 115","fulldoi":"https://doi.org/10.1073/pnas.1805847115","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"language":[{"iso":"eng"}],"scopus_import":"1","oa":1,"author":[{"last_name":"Kalinin","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"first_name":"Aldo","last_name":"Guzmán Sáenz","full_name":"Guzmán Sáenz, Aldo"},{"first_name":"Y","last_name":"Prieto","full_name":"Prieto, Y"},{"orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail"},{"first_name":"V","last_name":"Kalinina","full_name":"Kalinina, V"},{"full_name":"Lupercio, Ernesto","last_name":"Lupercio","first_name":"Ernesto"}],"department":[{"_id":"TaHa"}],"article_processing_charge":"No","volume":115,"oa_version":"Preprint","article_type":"original","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:26Z","date_updated":"2025-06-03T11:21:16Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"type":"journal_article","ec_funded":1,"page":"E8135 - E8142","isi":1,"month":"08","publist_id":"7990","doi":"10.1073/pnas.1805847115","date_published":"2018-08-28T00:00:00Z","arxiv":1,"external_id":{"arxiv":["1806.09153"],"isi":["000442861600009"]},"publication_identifier":{"issn":["0027-8424"]},"_id":"64","citation":{"apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115."},"day":"28","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_status":"published","year":"2018","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","status":"public"},{"article_number":"294","oa":1,"scopus_import":"1","department":[{"_id":"BeVi"}],"article_processing_charge":"No","author":[{"last_name":"Ma","full_name":"Ma, Wen","first_name":"Wen"},{"first_name":"Paris","full_name":"Veltsos, Paris","last_name":"Veltsos"},{"full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380"},{"first_name":"Nicolas","full_name":"Rodrigues, Nicolas","last_name":"Rodrigues"},{"first_name":"Roberto","last_name":"Sermier","full_name":"Sermier, Roberto"},{"last_name":"Jeffries","full_name":"Jeffries, Daniel","first_name":"Daniel"},{"last_name":"Perrin","full_name":"Perrin, Nicolas","first_name":"Nicolas"}],"language":[{"iso":"eng"}],"issue":"6","intvolume":" 9","fulldoi":"https://doi.org/10.3390/genes9060294","date_updated":"2024-12-11T13:13:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:45:09Z","oa_version":"Published Version","publisher":"MDPI","file_date_updated":"2020-07-14T12:45:22Z","ddc":["570"],"volume":9,"external_id":{"isi":["000436494200026"]},"doi":"10.3390/genes9060294","date_published":"2018-06-12T00:00:00Z","month":"06","publist_id":"7714","isi":1,"type":"journal_article","abstract":[{"lang":"eng","text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes."}],"year":"2018","status":"public","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","has_accepted_license":"1","publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:22Z","file_size":3985796,"date_created":"2019-02-01T07:52:28Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","relation":"main_file","file_id":"5905","file_name":"2018_Genes_Ma.pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"199","quality_controlled":"1","publication":"Genes","day":"12","citation":{"chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI, 2018. https://doi.org/10.3390/genes9060294.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI, 2018, doi:10.3390/genes9060294.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI, 2018.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI. https://doi.org/10.3390/genes9060294"}},{"oa_version":"Published Version","article_type":"original","publisher":"BioMed Central","ddc":["570"],"file_date_updated":"2020-07-14T12:45:23Z","volume":19,"related_material":{"record":[{"id":"9807","relation":"research_data","status":"public"},{"status":"public","id":"9808","relation":"research_data"}]},"date_updated":"2023-09-13T09:10:47Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:12Z","language":[{"iso":"eng"}],"issue":"1","intvolume":" 19","fulldoi":"https://doi.org/10.1186/s12864-018-5173-0","scopus_import":"1","oa":1,"department":[{"_id":"SiHi"}],"author":[{"first_name":"Juan","full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz"},{"last_name":"Karbiener","full_name":"Karbiener, Michael","first_name":"Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"last_name":"Gerhalter","full_name":"Gerhalter, Teresa","first_name":"Teresa"},{"last_name":"Herzig","full_name":"Herzig, Stephan","first_name":"Stephan"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2018_BMCGenomics_Higareda.pdf","file_id":"5712","relation":"main_file","checksum":"a56516e734dab589dc7f3e1915973b4d","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-17T14:52:57Z","file_size":4629784,"date_updated":"2020-07-14T12:45:23Z"}],"_id":"20","citation":{"apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0."},"day":"03","quality_controlled":"1","publication":"BMC Genomics","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","year":"2018","abstract":[{"lang":"eng","text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function."}],"status":"public","title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","isi":1,"month":"11","publist_id":"8035","type":"journal_article","external_id":{"isi":["000450976700002"]},"publication_identifier":{"issn":["1471-2164"]},"doi":"10.1186/s12864-018-5173-0","date_published":"2018-11-03T00:00:00Z"},{"ddc":["576"],"file_date_updated":"2020-07-14T12:45:23Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","date_created":"2018-12-11T11:45:10Z","related_material":{"record":[{"id":"563","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1074","relation":"part_of_dissertation"}]},"date_updated":"2026-04-08T14:06:37Z","pubrep_id":"963","fulldoi":"https://doi.org/10.15479/AT:ISTA:th_963","language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer","full_name":"Ringbauer, Harald"}],"supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"_id":"200","citation":{"apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.","mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963."},"alternative_title":["ISTA Thesis"],"day":"21","has_accepted_license":"1","publication_status":"published","file":[{"creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:14:55Z","access_level":"open_access","date_updated":"2020-07-14T12:45:23Z","file_size":5792935,"file_name":"IST-2018-963-v1+1_thesis.pdf","file_id":"5111","checksum":"8cc534d2b528ae017acf80874cce48c9","relation":"main_file"},{"access_level":"closed","date_created":"2019-04-05T09:30:12Z","content_type":"application/zip","creator":"dernst","file_size":113365,"date_updated":"2020-07-14T12:45:23Z","file_id":"6224","file_name":"2018_thesis_ringbauer_source.zip","relation":"source_file","checksum":"6af18d7e5a7e2728ceda2f41ee24f628"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"lang":"eng","text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm."}],"year":"2018","corr_author":"1","title":"Inferring recent demography from spatial genetic structure","status":"public","OA_place":"publisher","type":"dissertation","page":"146","month":"02","publist_id":"7713","date_published":"2018-02-21T00:00:00Z","doi":"10.15479/AT:ISTA:th_963","publication_identifier":{"issn":["2663-337X"]}}]